3O2X | pdb_00003o2x

MMP-13 in complex with selective tetrazole core inhibitor

PDB DOI: https://doi.org/10.2210/pdb3O2X/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-22 Released: 2011-08-10
Deposition Author(s): Kiefer, J.R., Barta, T.E., Becker, D.P., Mathis, K.J., Williams, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.210 (Depositor), 0.225 (DCC)
R-Value Work:
0.177 (Depositor), 0.192 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3O2X

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

MMP-13 in complex with selective tetrazole core inhibitor

Barta, T.E., Becker, D.P., Bedell, L.J., Hockerman, S.L., Kiefer, J.R., Li, M.H., Villamill, C.I., Rico, J.G., Mcdonald, J.J.

To be published.

Macromolecule Content

Total Structure Weight: 78.37 kDa
Atom Count: 6,167
Modeled Residue Count: 656
Deposited Residue Count: 656
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagenase 3	A, B, C, D	164	Homo sapiens	Mutation(s): 0 Gene Names: MMP13 EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45452 (Homo sapiens) Explore P45452 Go to UniProtKB: P45452
PHAROS: P45452 GTEx: ENSG00000137745
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45452
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3O2 Query on 3O2 Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain W [auth C] SDF format, chain N [auth B] SDF format, chain E [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain N [auth B] MOL2 format, chain E [auth A] mmCIF format, chain CA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain N [auth B] mmCIF format, chain E [auth A]	CA [auth D], E [auth A], N [auth B], W [auth C]	N-hydroxy-1-(2-methoxyethyl)-4-{[4-(3-{5-[4-(trifluoromethoxy)phenyl]-2H-tetrazol-2-yl}propoxy)phenyl]sulfonyl}piperidine-4-carboxamide C₂₆ H₃₁ F₃ N₆ O₇ S MTRATHZFTCSGDT-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain W [auth C]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain V [auth B] MOL2 format, chain M [auth A] MOL2 format, chain V [auth B] mmCIF format, chain M [auth A] mmCIF format, chain V [auth B]	M [auth A], V [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain V [auth B] Interactions & Density Focus chain M [auth A] Focus chain V [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain HA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth D]	BA [auth C] HA [auth D] IA [auth D] J [auth A] K [auth A] BA [auth C], HA [auth D], IA [auth D], J [auth A], K [auth A], L [auth A], S [auth B], T [auth B], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain P [auth B] SDF format, chain F [auth A] SDF format, chain EA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain P [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth D]	DA [auth D] EA [auth D] F [auth A] G [auth A] O [auth B] DA [auth D], EA [auth D], F [auth A], G [auth A], O [auth B], P [auth B], X [auth C], Y [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth C] Focus chain Y [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Z [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain AA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain AA [auth C]	AA [auth C] FA [auth D] GA [auth D] H [auth A] I [auth A] AA [auth C], FA [auth D], GA [auth D], H [auth A], I [auth A], Q [auth B], R [auth B], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.210 (Depositor), 0.225 (DCC)
R-Value Work: 0.177 (Depositor), 0.192 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.864	α = 90
b = 95.257	β = 90
c = 120.076	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-08-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-10
Type: Initial release
Version 1.1: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.